Example Sphynx Documentation

anat.py

#!/Library/Frameworks/EPD64.framework/Versions/Current/bin/python
import sys
import e_afni
import os
import commands
import nipype.pipeline.engine as pe
import nipype.algorithms.rapidart as ra
import nipype.interfaces.afni as afni
import nipype.interfaces.fsl as fsl
import nipype.interfaces.io as nio
import nipype.interfaces.utility as util



def create_anat_preproc():
    """ 
    Preprocessing of Anatomical(T1) Image
        
    Inputs ::
        inputspec.anat : anatomical runs ( filename or list of filenames)
    
    Outputs ::
        outputspec.refit : Deobliqued files
        outputspec.reorient : RPI oriented files
        outputspec.skullstrip : Skull Stripped RPI files
        outputspec.brain : Whole-Brain only mask files
    
    Example
    -------
    
    >>> prproc = create_anat_preproc()
    >>> preproc.inputs.inputspec.func=['sub1/rest_1/rest.nii.gz','sub2/rest_1/rest.nii.gz']
    >>> preporc.run() #doctest: +SKIP
        
    """
    preproc = pe.Workflow(name='anatpreproc')
    
    inputNode = pe.Node(util.IdentityInterface(fields=['anat']),
                        name='inputspec')
    
    outputNode = pe.Node(util.IdentityInterface(fields=['refit',
                                                    'reorient',
                                                    'skullstrip',
                                                    'brain']),
                         name='outputspec')
    
    anat_refit = pe.Node(interface=e_afni.Threedrefit(),
                         name='anat_refit')
    anat_refit.inputs.deoblique = True
    
    anat_reorient = pe.Node(interface=afni.Resample(),
                            name='anat_reorient')
    anat_reorient.inputs.orientation = 'RPI'
    
    anat_skullstrip = pe.Node(interface=afni.SkullStrip(),
                              name='anat_skullstrip')
    anat_skullstrip.inputs.options = '-o_ply'
    
    anat_calc = pe.Node(interface=e_afni.Threedcalc(),
                        name='anat_calc')
    anat_calc.inputs.expr = '\'a*step(b)\''
    
    preproc.connect(inputNode, 'anat',
                    anat_refit, 'in_file')
    preproc.connect(anat_refit, 'out_file',
                    anat_reorient, 'in_file')
    preproc.connect(anat_reorient, 'out_file',
                    anat_skullstrip, 'in_file')
    preproc.connect(anat_skullstrip, 'out_file',
                    anat_calc, 'infile_b')
    preproc.connect(anat_reorient, 'out_file',
                    anat_calc, 'infile_a')
    
    preproc.connect(anat_refit, 'out_file',
                    outputNode, 'refit')
    preproc.connect(anat_reorient, 'out_file',
                    outputNode, 'reorient')
    preproc.connect(anat_skullstrip, 'out_file',
                    outputNode, 'skullstrip')
    preproc.connect(anat_calc, 'out_file',
                    outputNode, 'brain')
    
    return preproc